Microcystis is a toxic colony-forming cyanobacterium, which can bloom in a wide range of freshwater ecosystems. Despite the ecological advantage of the colonial form, few studies have paid attention to the size of Microcystis colonies in the field. With the aim of evaluating the impact of a fluctuating physical environment on the colony size, the genotypic composition and the toxic potential of a Microcystis population, we investigated five different colony size classes of a Microcystis bloom in the Grangent reservoir (France). By sequencing the internal transcribed spacer of the ribosomal operon, we evidenced changes in the genetic structure among size classes in response to environmental change. While similar genotypes were seen in every size class in stable conditions, new dominant genotypes appeared in the smallest colonies (< 160 μm) concomitantly with mixing conditions, strongly suggesting the importance of these colonies in response to disturbances. Moreover, these small colonies played a major role in microcystin production during this bloom, since very high microcystin contents (> 1 pg.cell.−1) were found in their cells. These findings indicate that the colony size distribution of a Microcystis population in response to disturbance could be an adaptive strategy that may explain its ecological success in freshwater ecosystems.